Chromatin immunoprecipitations were performed using HFKs, CIN612 cells, or stable HFK 31 cells in the presence or absence of HU. Cells were cultured as described above. Chromatin immunoprecipitation was performed using γ-H2AX (Millipore; catalog no. 05-636), RAD51 (Millipore; catalog no. 05-530-I), BRCA1 (Thermo Fisher; catalog no. MA1-23164), SMC-1 (Abcam, Inc.; catalog no. ab9262), and normal mouse IgG antibody (Santa Cruz; catalog no. SC-2025). Protocol was performed as previously described (37 (link)).
Real-time PCR was performed with a LightCycler 480 system (Roche) using HPV 31 URR primers, Alu primers, or HPV 31 L2 primers as follows: URR Forward, 5′-AAC|TGC|CAA|GGT|TGT|GTC|ATG|C-3′; URR Reverse, 5′-TGG|CGT|CTG|TAG|GTT|TGC|AC-3′; Alu Forward, 5′-ACG|AGG|TCA|GGA|GAT|CGA|GA-3′; Alu Reverse, 5′-CTC|AGC|CTC|CCA|AGT|AGC|TG-3′; L2 Forward, 5′-TTT|GGT|GGG|TTG|GGT|ATT|GG-3′; L2 Reverse, 5′-GTA|GGA|GGC|TGC|AAT|ACA|GAT|G-3′. All primers were determined to have similar levels of efficiency based on the methods previously described by Livak et al. (38 (link)).
Real-time PCR was performed with a LightCycler 480 system (Roche) using HPV 31 URR primers, Alu primers, or HPV 31 L2 primers as follows: URR Forward, 5′-AAC|TGC|CAA|GGT|TGT|GTC|ATG|C-3′; URR Reverse, 5′-TGG|CGT|CTG|TAG|GTT|TGC|AC-3′; Alu Forward, 5′-ACG|AGG|TCA|GGA|GAT|CGA|GA-3′; Alu Reverse, 5′-CTC|AGC|CTC|CCA|AGT|AGC|TG-3′; L2 Forward, 5′-TTT|GGT|GGG|TTG|GGT|ATT|GG-3′; L2 Reverse, 5′-GTA|GGA|GGC|TGC|AAT|ACA|GAT|G-3′. All primers were determined to have similar levels of efficiency based on the methods previously described by Livak et al. (38 (link)).
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